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1.
Gene ; 718: 144018, 2019 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-31454543

RESUMO

Cytosine DNA methylation (5mC) is an epigenetic mark that regulates gene expression in plant responses to environmental stresses. Zinc-finger protein (ZFP) is the largest family of DNA-binding transcription factors that also plays an essential role in eukaryote. In plant we have already identified and characterized different useful ZFP-genes. While, the main objective of this research was to observe and identify more targeted stress responsive genes of ZFPs epigenetically throughout genome in rice for the first time. A comprehensive correlation analysis was performed through methylated DNA immunoprecipitation (MeDIP)-chip hybridization in rice under salt and osmotic stresses. High salinity and drought are two major abiotic hazards that are destroying the crop world-wide. As a result, Through-out genome 14 unique stress responsive transcription factors of ZFP-genes with varying level of methylation and expression under two conditions (control vs. stress) were isolated. All the identified genes were confirmed from different databases for their specific structure, cis-regulatory elements, phylogenetic analysis, and synteny analysis. Moreover, the tissue-specific expression patterns, and expression under abiotic and phytohormones stresses were also investigated. Phylogenetically all the genes were divided into 6 distinct subgroups with Arabidopsis and orthologous proteins were find-out through synteny analysis. Available RNA-seq data in response to various phytohormones provided hormone inducible gene expression profile. Through Reverse Transcriptase qPCR (RT-qPCR) analysis tissue-specific expression in shoot and root over various time points against salt and osmotic stresses exhibited the diverse expression patterns of identified genes. Overall, the present study providing a foundation for in-depth characterization of identified genes and to further understand the epigenetic role of DNA methylation for genes expression and environmental stresses regulation in higher plant.


Assuntos
Metilação de DNA/fisiologia , DNA de Plantas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/fisiologia , Oryza , Proteínas de Plantas , Estresse Fisiológico/fisiologia , Fatores de Transcrição , DNA de Plantas/genética , DNA de Plantas/metabolismo , Estudo de Associação Genômica Ampla , Oryza/genética , Oryza/metabolismo , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Fatores de Transcrição/classificação , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
2.
Cell Mol Life Sci ; 76(19): 3753-3764, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31161283

RESUMO

Nitrogen (N) is one of the most important essential macro-elements for plant growth and development, and nitrate represents the most abundant inorganic form of N in soils. The nitrate uptake and assimilation processes are finely tuned according to the available nitrate in the surroundings as well as by the internal finely coordinated signaling pathways. The NIN-like proteins (NLPs) harbor both RWP-RK, and Phox and Bem1 (PB1) domains, and they belong to the well-characterized plant-specific RWP-RK transcription factor gene family. NLPs are known to be involved in the nitrate signaling pathway by activating downstream target genes, and thus they are implicated in the primary nitrate response in the nucleus via their RWP-RK domains. The PB1 domain is a ubiquitous protein-protein interaction domain and it comprises another regulatory layer for NLPs via the protein interactions within NLPs or with other essential components. Recently, Ca2+-Ca2+ sensor protein kinase-NLP signaling cascades have been identified and they allow NLPs to have central roles in mediating the nitrate signaling pathway. NLPs play essential roles in many aspects of plant growth and development via the finely tuned nitrate signaling pathway. Furthermore, recent studies have highlighted the emerging roles played by NLPs in the N starvation response, nodule formation in legumes, N and P interactions, and root cap release in higher plants. In this review, we consider recent advances in the identification, evolution, molecular characteristics, and functions of the NLP gene family in plant growth and development.


Assuntos
Nitratos/metabolismo , Proteínas de Plantas/fisiologia , Fatores de Transcrição/fisiologia , Evolução Biológica , Nitrogênio/metabolismo , Fosfatos/metabolismo , Desenvolvimento Vegetal , Proteínas de Plantas/química , Proteínas de Plantas/classificação , Nodulação , Plantas/metabolismo , Transdução de Sinais , Fatores de Transcrição/química , Fatores de Transcrição/classificação
3.
Food Chem ; 292: 143-150, 2019 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-31054659

RESUMO

The effect of eugenol (EUG) on chilling injury (CI) to eggplant fruit (Solanum melongena L.) was investigated. Eggplant fruit were pre-treated with 25 µL/L EUG, and then stored at 4 °C for 12 days. Results showed that EUG fumigation treatment effectively retarded the CI development, reduced pulp browning, weight loss, and malondialdehyde (MDA) content, and sustained soluble solids content (SSC) and proline content. Moreover, the activities of polyphenol oxidase (PPO) and peroxidase (POD) were inhibited by EUG. C-repeat/dehydration-responsive element binding factors (CBF) genes are transcription factors playing a critical role in cold acclimation. To illuminate the molecular regulation of EUG on chilling tolerance in eggplant fruit, a 1151 bp SmCBF gene was identified and the effect of EUG on SmCBF expression was determined by RT-qPCR. EUG resulted in a higher SmCBF expression. These findings suggested that EUG treatment had potential effect on alleviating CI in eggplant fruit.


Assuntos
Eugenol/farmacologia , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Proteínas de Plantas/metabolismo , Solanum melongena/genética , Fatores de Transcrição/metabolismo , Sequência de Aminoácidos , Temperatura Baixa , Armazenamento de Alimentos , Frutas/efeitos dos fármacos , Frutas/genética , Frutas/metabolismo , Fumigação , Malondialdeído/metabolismo , Fenóis/análise , Filogenia , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , RNA de Plantas/química , RNA de Plantas/isolamento & purificação , RNA de Plantas/metabolismo , Alinhamento de Sequência , Solanum melongena/metabolismo , Fatores de Transcrição/classificação , Fatores de Transcrição/genética
4.
BMC Genomics ; 20(1): 326, 2019 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31035917

RESUMO

BACKGROUND: Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subjecting proteins to hydrolysis by the UPS. Recently, it has been demonstrated that a specific class of E3 ligases termed the U-box ligases are directly associated with the defense mechanisms against abiotic and biotic stresses in several plants. However, no studies on U-box E3 ligases have been performed in one of the important staple crops, barley. RESULTS: In this study, we identified 67 putative U-box E3 ligases from the barley genome and expressed sequence tags (ESTs). Similar to Arabidopsis and rice U-box E3 ligases, most of barley U-box E3 ligases possess evolutionary well-conserved domain organizations. Based on the domain compositions and arrangements, the barley U-box proteins were classified into eight different classes. Along with this new classification, we refined the previously reported classifications of U-box E3 ligase genes in Arabidopsis and rice. Furthermore, we investigated the expression profile of 67 U-box E3 ligase genes in response to drought stress and pathogen infection. We observed that many U-box E3 ligase genes were specifically up-and-down regulated by drought stress or by fungal infection, implying their possible roles of some U-box E3 ligase genes in the stress responses. CONCLUSION: This study reports the classification of U-box E3 ligases in barley and their expression profiles against drought stress and pathogen infection. Therefore, the classification and expression profiling of barley U-box genes can be used as a platform to functionally define the stress-related E3 ligases in barley.


Assuntos
Regulação da Expressão Gênica de Plantas , Hordeum/genética , Interações Hospedeiro-Parasita/genética , Proteínas de Plantas/genética , Ubiquitina-Proteína Ligases/genética , Sequência de Aminoácidos , Arabidopsis/genética , Ascomicetos/patogenicidade , Secas , Genoma de Planta , Hordeum/crescimento & desenvolvimento , Oryza/genética , Filogenia , Proteínas de Plantas/classificação , Plântula/microbiologia , Alinhamento de Sequência , Ubiquitina-Proteína Ligases/classificação
5.
Comput Biol Chem ; 80: 341-350, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31082717

RESUMO

MADS-box genes comprise a family of transcription factors that function in the growth and development of plants. To obtain insights into their evolution in watermelon (Citrullus lanatus), we carried out a genome-wide analysis and identified 39 MADS-box genes. These genes were classified into MIKCc (25), MIKC*(3), Mα (5), Mß (3), and Mγ (3) clades according to their phylogenetic relationship with Arabidopsis thaliana and Cucumis sativus; moreover, these 25 genes in the MIKC clade could be classified into 13 subfamilies, and the Flowering Locus C (FLC) subfamily is absent in watermelon. Analysis of the conserved gene motifs showed similar motifs among clades. Continuing chromosomal localizations analysis indicated that MADS-box genes were distributed across 11 chromosomes in watermelon, and these genes were conditioned to be differentially expressed during plant growth and development. This research provides information that will aid further investigations into the evolution of the MADS-box gene family in plants.


Assuntos
Citrullus/genética , Genes de Plantas , Proteínas de Domínio MADS/genética , Proteínas de Plantas/genética , Arabidopsis/genética , Cucumis sativus/genética , Expressão Gênica , Perfilação da Expressão Gênica , Proteínas de Domínio MADS/classificação , Filogenia , Proteínas de Plantas/classificação , Transcriptoma
6.
BMC Plant Biol ; 19(1): 223, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31138149

RESUMO

BACKGROUND: MADS-box genes play crucial roles in plant floral organ formation and plant reproductive development. However, there is still no information on genome-wide identification and classification of MADS-box genes in some representative plant species. A comprehensive investigation of MIKC-type genes in the orchid Dendrobium officinale is still lacking. RESULTS: Here we conducted a genome-wide analysis of MADS-box proteins from 29 species. In total, 1689 MADS-box proteins were identified. Two types of MADS-box genes, termed type I and II, were found in land plants, but not in liverwort. The SQUA, DEF/GLO, AG and SEP subfamilies existed in all the tested flowering plants, while SQUA was absent in the gymnosperm Ginkgo biloba, and no genes of the four subfamilies were found in a charophyte, liverwort, mosses, or lycophyte. This strongly corroborates the notion that clades of floral organ identity genes led to the evolution of flower development in flowering plants. Nine subfamilies of MIKCC genes were present in two orchids, D. officinale and Phalaenopsis equestris, while the TM8, FLC, AGL15 and AGL12 subfamilies may be lost. In addition, the four clades of floral organ identity genes in both orchids displayed a conservative and divergent expression pattern. Only three MIKC-type genes were induced by cold stress in D. officinale while 15 MIKC-type genes showed different levels of expression during seed germination. CONCLUSIONS: MIKC-type genes were identified from streptophyte lineages, revealing new insights into their evolution and development relationships. Our results show a novel role of MIKC-type genes in seed germination and provide a useful clue for future research on seed germination in orchids.


Assuntos
Proteínas de Domínio MADS/análise , Proteínas de Plantas/análise , Estreptófitas/genética , Dendrobium/genética , Genes de Plantas , Estudo de Associação Genômica Ampla , Proteínas de Domínio MADS/classificação , Família Multigênica , Orchidaceae/genética , Proteínas de Plantas/classificação
7.
Gene ; 702: 89-98, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-30928363

RESUMO

Teosinte branched 1/Cycloidea/Proliferating cell factor 1 (TCP) proteins belongs to a plant-specific transcription factor family that plays important roles in plant development. TCP gene-regulated plant branching occurs downstream in the strigolactone pathway. In this study, 41 TCP genes were identified in the genome of Panicum virgatum L. (switchgrass). These genes all contained the TCP conserved domain, and they belonged to two subfamilies distributed across 18 chromosomes. Analysis of gene expression using RNA-Seq data showed that 16 TCP genes were highly expressed in the inflorescence and shoot. The expression patterns of 13 selected PvTCP genes were analyzed in different tissues, and their responses to strigolactones (SLs) were examined. The selected genes were expressed differentially in a range of tissues and to application of SLs, indicating that PvTCPs were involved in a range of developmental and physiological processes. This genome-wide analysis and determination of PvTCP gene-expression patterns yielded valuable information on switchgrass development that will inform studies into improving switchgrass and other species for crop production.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Família Multigênica , Panicum/genética , Proteínas de Plantas/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/química , Fatores de Transcrição Hélice-Alça-Hélice Básicos/classificação , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Cromossomos de Plantas , Genes de Plantas , Panicum/metabolismo , Reguladores de Crescimento de Planta/farmacologia , Proteínas de Plantas/química , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , Sintenia
8.
Molecules ; 24(8)2019 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-31018578

RESUMO

Legume crops represent the major source of food protein and contribute to human nutrition and animal feeding. An essential improvement of their productivity can be achieved by symbiosis with beneficial soil microorganisms-rhizobia (Rh) and arbuscular mycorrhizal (AM) fungi. The efficiency of these interactions depends on plant genotype. Recently, we have shown that, after simultaneous inoculation with Rh and AM, the productivity gain of pea (Pisum sativum L) line K-8274, characterized by high efficiency of interaction with soil microorganisms (EIBSM), was higher in comparison to a low-EIBSM line K-3358. However, the molecular mechanisms behind this effect are still uncharacterized. Therefore, here, we address the alterations in pea seed proteome, underlying the symbiosis-related productivity gain, and identify 111 differentially expressed proteins in the two lines. The high-EIBSM line K-8274 responded to inoculation by prolongation of seed maturation, manifested by up-regulation of proteins involved in cellular respiration, protein biosynthesis, and down-regulation of late-embryogenesis abundant (LEA) proteins. In contrast, the low-EIBSM line K-3358 demonstrated lower levels of the proteins, related to cell metabolism. Thus, we propose that the EIBSM trait is linked to prolongation of seed filling that needs to be taken into account in pulse crop breeding programs. The raw data have been deposited to the ProteomeXchange with identifier PXD013479.


Assuntos
Regulação da Expressão Gênica de Plantas , Ervilhas/genética , Proteínas de Plantas/isolamento & purificação , Proteoma/isolamento & purificação , Sementes/genética , Simbiose/genética , Bactérias/crescimento & desenvolvimento , Biomassa , Cromatografia Líquida de Alta Pressão , Fungos/fisiologia , Ontologia Genética , Genótipo , Redes e Vias Metabólicas/genética , Anotação de Sequência Molecular , Micorrizas/fisiologia , Ervilhas/química , Ervilhas/metabolismo , Ervilhas/microbiologia , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Nodulação/genética , Proteoma/classificação , Proteoma/genética , Proteômica/métodos , Sementes/química , Sementes/metabolismo , Microbiologia do Solo , Espectrometria de Massas em Tandem
9.
Int J Mol Sci ; 20(8)2019 Apr 21.
Artigo em Inglês | MEDLINE | ID: mdl-31010077

RESUMO

Purple acid phosphatase (PAP) encoding genes are a multigene family. PAPs require iron (Fe) to exert their functions that are involved in diverse biological roles including Fe homeostasis. However, the possible roles of PAPs in response to excess Fe remain unknown. In this study, we attempted to understand the regulation of PAPs by excess Fe in tea plant (Camellia sinensis). A genome-wide investigation of PAP encoding genes identified 19 CsPAP members based on the conserved motifs. The phylogenetic analysis showed that PAPs could be clustered into four groups, of which group II contained two specific cysteine-containing motifs "GGECGV" and "YERTC". To explore the expression patterns of CsPAP genes in response to excessive Fe supply, RNA-sequencing (RNA-seq) analyses were performed to compare their transcript abundances between tea plants that are grown under normal and high iron conditions, respectively. 17 members were shown to be transcribed in both roots and leaves. When supplied with a high amount of iron, the expression levels of four genes were significantly changed. Of which, CsPAP15a, CsPAP23 and CsPAP27c were shown as downregulated, while the highly expressed CsPAP10a was upregulated. Moreover, CsPAP23 was found to be alternatively spliced, suggesting its post-transcriptional regulation. The present work implicates that some CsPAP genes could be associated with the responses of tea plants to the iron regime, which may offer a new direction towards a further understanding of iron homeostasis and provide the potential approaches for crop improvement in terms of iron biofortification.


Assuntos
Fosfatase Ácida/genética , Camellia sinensis/enzimologia , Glicoproteínas/genética , Ferro/metabolismo , Proteínas de Plantas/genética , Fosfatase Ácida/classificação , Fosfatase Ácida/metabolismo , Sequência de Aminoácidos , Camellia sinensis/genética , Genes de Plantas , Glicoproteínas/classificação , Glicoproteínas/metabolismo , Família Multigênica , Filogenia , Folhas de Planta/enzimologia , Folhas de Planta/genética , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , Raízes de Plantas/enzimologia , Raízes de Plantas/genética , Processamento de RNA , Alinhamento de Sequência , Transcriptoma
10.
Int J Mol Sci ; 20(8)2019 Apr 14.
Artigo em Inglês | MEDLINE | ID: mdl-31013972

RESUMO

Paclitaxel is an important anticancer drug. The phytohormone jasmonic acid can significantly induce the biosynthesis of paclitaxel in Taxus, but the molecular mechanism has not yet been resolved. To establish the jasmonic acid signalling pathway of Taxus media, based on the gene of the jasmonic acid signalling pathway of Arabidopsis thaliana, sequence analysis was performed to isolate the jasmonic acid signal from the transcriptome, a transcriptional cluster of pathway gene homologs and the full length of 22 genes were obtained by RACE PCR at 5' and 3': two EI ubiquitin ligase genes, COI1-1 and COI1-2;7 MYC bHLH type transcription factor (MYC2, MYC3, MYC4, JAM1, JAM2, EGL3, TT8); 12 JAZ genes containing the ZIM domain; and MED25, one of the components of the transcriptional complex. The protein interaction between each were confirmed by yeast two hybridization and bimolecular fluorescence complementation based on similar genes interaction in Arabidopsis. A similar jasmonate signaling pathway was illustrated in T. media. All known paclitaxel biosynthesis genes promoters were isolated by genome walker PCR. To investigate the jasmonate signaling effect on these genes' expression, the transcription activity of MYC2, MYC3 and MYC4 on these promoters were examined. There are 12, 10 and 11 paclitaxel biosynthesis genes promoters that could be activated by MYC2, MYC3 and MYC4.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Ciclopentanos/metabolismo , Oxilipinas/metabolismo , Paclitaxel/biossíntese , Proteínas de Plantas/metabolismo , Taxus/metabolismo , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Fatores de Transcrição Hélice-Alça-Hélice Básicos/classificação , Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Filogenia , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Regiões Promotoras Genéticas , Transdução de Sinais , Técnicas do Sistema de Duplo-Híbrido
11.
BMC Genomics ; 20(1): 257, 2019 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-30935363

RESUMO

BACKGROUND: Enhancement of crop productivity under various abiotic stresses is a major objective of agronomic research. Wheat (Triticum aestivum L.) as one of the world's staple crops is highly sensitive to heat stress, which can adversely affect both yield and quality. Plant heat shock factors (Hsfs) play a crucial role in abiotic and biotic stress response and conferring stress tolerance. Thus, multifunctional Hsfs may be potentially targets in generating novel strains that have the ability to survive environments that feature a combination of stresses. RESULT: In this study, using the released genome sequence of wheat and the novel Hsf protein HMM (Hidden Markov Model) model constructed with the Hsf protein sequence of model monocot (Oryza sativa) and dicot (Arabidopsis thaliana) plants, genome-wide TaHsfs identification was performed. Eighty-two non-redundant and full-length TaHsfs were randomly located on 21 chromosomes. The structural characteristics and phylogenetic analysis with Arabidopsis thaliana, Oryza sativa and Zea mays were used to classify these genes into three major classes and further into 13 subclasses. A novel subclass, TaHsfC3 was found which had not been documented in wheat or other plants, and did not show any orthologous genes in A. thaliana, O. sativa, or Z. mays Hsf families. The observation of a high proportion of homeologous TaHsf gene groups suggests that the allopolyploid process, which occurred after the fusion of genomes, contributed to the expansion of the TaHsf family. Furthermore, TaHsfs expression profiling by RNA-seq revealed that the TaHsfs could be responsive not only to abiotic stresses but also to phytohormones. Additionally, the TaHsf family genes exhibited class-, subclass- and organ-specific expression patterns in response to various treatments. CONCLUSIONS: A comprehensive analysis of Hsf genes was performed in wheat, which is useful for better understanding one of the most complex Hsf gene families. Variations in the expression patterns under different abiotic stress and phytohormone treatments provide clues for further analysis of the TaHsfs functions and corresponding signal transduction pathways in wheat.


Assuntos
Genoma de Planta , Fatores de Transcrição de Choque Térmico/genética , Proteínas de Plantas/genética , Estresse Fisiológico , Triticum/genética , Sequência de Aminoácidos , Arabidopsis/genética , Loci Gênicos , Fatores de Transcrição de Choque Térmico/classificação , Fatores de Transcrição de Choque Térmico/metabolismo , Oryza/genética , Filogenia , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , RNA de Plantas/química , RNA de Plantas/isolamento & purificação , RNA de Plantas/metabolismo , Alinhamento de Sequência , Análise de Sequência de RNA , Transcriptoma , Zea mays/genética
12.
BMC Genomics ; 20(1): 256, 2019 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-30935385

RESUMO

BACKGROUND: Histone methylation mainly occurs on the lysine residues and plays a crucial role during flowering and stress responses of plants, through changing the methylation status or ratio of lysine residues. Histone lysine residues of plants can arise in three forms of methylation (single, double and triple) and the corresponding demethylation can also ensue on certain occasions, by which the plants can accommodate the homeostasis of histone methylation by means of lysine methyltransferase and demethylase. The JmjC domain-containing proteins, an important family of histone lysine demethylases, play a vital role in maintaining homeostasis of histone methylation in vivo. RESULTS: In this study, we have identified 19 JmjC domain-containing histone demethylase (JHDM) proteins in maize. Based on structural characteristics and a comparison of phylogenetic relationships of JHDM gene families from Arabidopsis, rice and maize, all 19 JHDM proteins in maize were categorized into three different subfamilies. Furthermore, chromosome location and schematic structure revealed an unevenly distribution on chromosomes and structure features of ZmJMJ genes in maize, respectively. Eventually, the 19 ZmJMJ genes displayed different expression patterns at diverse developmental stages of maize based on transcriptome analysis. Further, quantitative real-time PCR analysis showed that all 19 ZmJMJ genes were responsive to heat stress treatment, suggesting their potential roles in heat stress response. CONCLUSIONS: Overall, our study will serve to present an important theoretical basis for future functional verification of JHDM genes to further unravel the mechanisms of epigenetic regulation in plants.


Assuntos
Genoma de Planta , Histona Desmetilases com o Domínio Jumonji/metabolismo , Proteínas de Plantas/metabolismo , Zea mays/genética , Arabidopsis/genética , Análise por Conglomerados , Loci Gênicos , Histonas/metabolismo , Histona Desmetilases com o Domínio Jumonji/classificação , Histona Desmetilases com o Domínio Jumonji/genética , Metilação , Oryza/genética , Filogenia , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Regiões Promotoras Genéticas , Transcriptoma
13.
Gene ; 702: 133-142, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-30904717

RESUMO

Phosphofructokinase plays an essential role in sugar metabolism in plants. Plants possess two types of phosphofructokinase proteins for phosphorylation of fructose-6-phosphate, the pyrophosphate-dependent fructose-6-phosphate phosphotransferase (PFP), and the ATP-dependent phosphofructokinase (PFK). Until now, the gene evolution, expression patterns, and functions of phosphofructokinase proteins were unknown in pear. In this report, 14 phosphofructokinase genes were identified in pear. The phylogenetic tree indicated that the phosphofructokinase gene family could be grouped into two subfamilies, with 10 genes belonging to the PbPFK subfamily, and 4 genes belonging to the PbPFP subfamily. Conserved motifs and exon numbers of the phosphofructokinase were found in pear and other six species. The evolution analysis indicated that WGD/Segmental and dispersed duplications were the main duplication models for the phosphofructokinase genes expansion in pear and other six species. Analysis of cis-regulatory element sequences of all phosphofructokinase genes identified light regulation and the MYB binding site in the promoter of all pear phosphofructokinase genes, suggesting that phosphofructokinase might could be regulated by light and MYB transcription factors (TFs). Gene expression patterns revealed that PbPFP1 showed similar pattern with sorbitol contents, suggesting important contributions to sugar accumulation during fruit development. Further functional analysis indicated that the phosphofructokinase gene PbPFP1 was localized on plasma membrane compartment, indicating that PbPFP1 had function in plasma membrane. Transient transformation of PbPFP1 in pear fruits led to significant increases of fructose and sorbitol compared to controls. Overall, our study provides important insights into the gene expression patterns and important potential functions of phosphofructokinase for sugar accumulation in pear fruits, which will help to enrich understanding of sugar-related bio-pathways and lay the molecular basis for fruit quality improvement.


Assuntos
Família Multigênica , Fosfofrutoquinases/classificação , Fosfofrutoquinases/genética , Pyrus/enzimologia , Motivos de Aminoácidos , Membrana Celular/enzimologia , Mapeamento Cromossômico , Éxons , Frutas/enzimologia , Frutas/genética , Frutas/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Íntrons , Fosfofrutoquinases/química , Fosfofrutoquinases/metabolismo , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Regiões Promotoras Genéticas , Pyrus/classificação , Pyrus/genética , Pyrus/crescimento & desenvolvimento , Rosaceae/classificação , Açúcares/metabolismo , Transcrição Genética
14.
Plant Cell Rep ; 38(5): 637-655, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30747272

RESUMO

KEY MESSAGE: Six Sec14-like PITP genes from sugarcane were identified, two of them were cloned, and their biological functions were characterized indicating their involvement in plant defense against biotic and abiotic stresses. Sec14, a phosphatidylinositol transfer protein (PITP) is widely present in eukaryotes. In this study, the structure and expression patterns of six Sec14-like PITP genes (ScSEC14-1, ScSEC14p, ScSFH1, ScSFH2, ScPATL1, and ScPATL2) from sugarcane were analyzed, and two of them (ScSEC14-1 and ScSEC14p) were cloned and functionally verified. Phylogenetic analysis divided these genes into four groups, including group I (ScSFH1 and ScSFH2), group II (ScPATL1 and ScPATL2), Group III (ScSEC14p), and group V (ScSEC14-1). qRT-PCR analysis showed tissue-specific expression of these genes, primarily in the root, leaf, and bud tissues. They responded differently to SA, MeJA, and ABA stresses. ScSEC14-1, ScSEC14p, and ScSFH2 were upregulated by CuCl2 and CdCl2, while ScSEC14-1, ScSFH1, ScSFH2, and ScPATL1 were upregulated by PEG and NaCl. When infected by Sporisorium scitamineum, the transcripts of ScSFH1, ScSFH2, ScPATL1, and ScPATL2 were upregulated in the resistant genotype Yacheng 05-179, while those of ScSEC14-1 and ScSEC14p were upregulated in the susceptible genotype ROC22. Subcellular localization showed that ScSEC14-1 and ScSEC14p were mainly localized in the plasma membrane and cytoplasm. Enhanced growth of Escherichia coli BL21 cells expressing ScSEC14-1 and ScSEC14p showed high tolerance to NaCl and mannitol stresses. The transient overexpression of ScSEC14-1 and ScSEC14p in Nicotiana benthamiana leaves enhanced its resistance to the infection of tobacco pathogens Ralstonia solanacearum and Fusarium solani var. coeruleum. We can conclude the involvement of ScSEC14-1 and ScSEC14p in the defense against biotic and abiotic stresses, which should facilitate further research on Sec14-like PITP gene family, especially its regulatory mechanisms in sugarcane.


Assuntos
Saccharum/metabolismo , Secas , Regulação da Expressão Gênica de Plantas , Filogenia , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética , Estresse Fisiológico/fisiologia
15.
Mol Phylogenet Evol ; 134: 99-110, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30711535

RESUMO

Calreticulin (CRT) is an multifunctional resident endoplasmic reticulum (ER) luminal protein implicated in regulating a variety of cellular processes, including Ca2+ storage/mobilization and protein folding. These multiple functions may be carried out by different CRT genes and protein isoforms. The plant CRT family consist of three genes: CRT1 and CRT2 classified in the common subclass (CRT1/2), and CRT3. These genes are highly conserved during evolution and encode three different protein products (CRT1, 2 and 3). The aim of the current study was to conduct a comparative analysis and sequence-based classification of the plant CRT genes. We used nucleotide and amino acid sequences to phylogenetically cluster the genes and examine potential glycosylation patterns. Additionally, we analyzed phylogenetic relationships within the CRT subclasses. Finally, we analyzed intraspecific CRT duplication events among mono- and dicotyledon species. Our results confirm that each of the CRT genes exist in multiple copies in plant genomes, and that CRT gene duplication is a widespread process in plants.


Assuntos
Calreticulina/classificação , Filogenia , Proteínas de Plantas/classificação , Homologia de Sequência de Aminoácidos , Sequência de Aminoácidos , Calreticulina/genética , Proteínas de Plantas/genética
16.
Planta ; 249(5): 1301-1318, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-30617544

RESUMO

MAIN CONCLUSION: Genome-wide identification, expression analysis and potential functional characterization of previously uncharacterized MADS family of tartary buckwheat, emphasized the importance of this gene family in plant growth and development. The MADS transcription factor is a key regulatory factor in the development of most plants. The MADS gene in plants controls all aspects of tissue and organ growth and reproduction and can be used to regulate plant seed cracking. However, there has been little research on the MADS genes of tartary buckwheat (Fagopyrum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allows us to study the tissue and expression profiles of the MADS gene in tartary buckwheat at a genome-wide level. In this study, 65 MADS genes of tartary buckwheat were identified and renamed according to the chromosomal distribution of the FtMADS genes. Here, we provide a complete overview of the gene structure, gene expression, genomic mapping, protein motif organization, and phylogenetic relationships of each member of the gene family. According to the phylogenetic relationship of MADS genes, the transcription factor family was divided into two subfamilies, the M subfamily (28 genes) and the MIKC subfamily (37 genes). The results showed that the FtMADS genes belonged to related sister pairs and the chromosomal map showed that the replication of FtMADSs was related to the replication of chromosome blocks. In different tissues and at different fruit development stages, the FtMADS genes obtained by real-time quantitative PCR (RT-qPCR) showed obvious expression patterns. A comprehensive analysis of the MADS genes in tartary buckwheat was conducted. Through systematic analysis, the potential genes that may regulate the growth and development of tartary buckwheat and the genes that may regulate the easy dehulling of tartary buckwheat fruit were screened, which laid a solid foundation for improving the quality of tartary buckwheat.


Assuntos
Fagopyrum/metabolismo , Frutas/metabolismo , Proteínas de Plantas/metabolismo , Fagopyrum/genética , Frutas/genética , Regulação da Expressão Gênica de Plantas , Filogenia , Proteínas de Plantas/classificação , Proteínas de Plantas/genética
17.
BMC Genomics ; 20(1): 83, 2019 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-30678642

RESUMO

BACKGROUND: Sugarcane served as the model plant for discovery of the C4 photosynthetic pathway. Magnesium is the central atom of chlorophyll, and thus is considered as a critical nutrient for plant development and photosynthesis. In plants, the magnesium transporter (MGT) family is composed of a number of membrane proteins, which play crucial roles in maintaining Mg homeostasis. However, to date there is no information available on the genomics of MGTs in sugarcane due to the complexity of the Saccharum genome. RESULTS: Here, we identified 10 MGTs from the Saccharum spontaneum genome. Phylogenetic analysis of MGTs suggested that the MGTs contained at least 5 last common ancestors before the origin of angiosperms. Gene structure analysis suggested that MGTs family of dicotyledon may be accompanied by intron loss and pseudoexon phenomena during evolution. The pairwise synonymous substitution rates corresponding to a divergence time ranged from 142.3 to 236.6 Mya, demonstrating that the MGTs are an ancient gene family in plants. Both the phylogeny and Ks analyses indicated that SsMGT1/SsMGT2 originated from the recent ρWGD, and SsMGT7/SsMGT8 originated from the recent σ WGD. These 4 recently duplicated genes were shown low expression levels and assumed to be functionally redundant. MGT6, MGT9 and MGT10 weredominant genes in the MGT family and werepredicted to be located inthe chloroplast. Of the 3 dominant MGTs, SsMGT6 expression levels were found to be induced in the light period, while SsMGT9 and SsMTG10 displayed high expression levels in the dark period. These results suggested that SsMGT6 may have a function complementary to SsMGT9 and SsMTG10 that follows thecircadian clock for MGT in the leaf tissues of S. spontaneum. MGT3, MGT7 and MGT10 had higher expression levels Insaccharum officinarum than in S. spontaneum, suggesting their functional divergence after the split of S. spontaneum and S. officinarum. CONCLUSIONS: This study of gene evolution and expression of MGTs in S. spontaneum provided basis for the comprehensive genomic study of the entire MGT genes family in Saccharum. The results are valuable for further functional analyses of MGT genes and utilization of the MGTs for Saccharum genetic improvement.


Assuntos
Proteínas de Transporte de Cátions/genética , Evolução Molecular , Magnésio/metabolismo , Família Multigênica , Proteínas de Plantas/genética , Saccharum/genética , Proteínas de Transporte de Cátions/classificação , Proteínas de Transporte de Cátions/metabolismo , Ritmo Circadiano , Éxons , Expressão Gênica/efeitos dos fármacos , Genes de Plantas , Genômica , Íntrons , Filogenia , Reguladores de Crescimento de Planta/farmacologia , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , Saccharum/efeitos dos fármacos , Saccharum/crescimento & desenvolvimento , Saccharum/metabolismo
18.
Plant Mol Biol ; 99(4-5): 449-460, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30689141

RESUMO

KEY MESSAGE: This report reveals that the LMI1-like and KNOX1 genes coordinately control the leaf development and different combinations of those genes which produce diverse leaf shapes including broad, lobed and compound leaves. Class I KNOTTED1-like homeobox (KNOX1) genes are involved in compound leaf development and are repressed by the ASYMMETRIC LEAVES1 (AS1)-AS2 complex. Cotton plants have a variety of leaf shapes, including broad leaves and lobed leaves. GhOKRA, a LATE MERISTEM IDENTITY 1 (LMI1)-like gene, controls the development of an okra leaf shape. We cloned the corresponding cotton homologs of Arabidopsis thaliana AS1 and AS2 and seven KNOX1 genes. Through virus-induced gene silencing technology, we found that either GhAS1 or GhAS2-silenced cotton plants showed a great change in leaf shape from okra leaves to trifoliolate dissected leaves. In the shoot tips of these plants, the expression of the cotton ortholog of Knotted in A. thaliana 1 (KNAT1), GhKNOTTED1-LIKE2/3/4 (GhKNL2/3/4), was increased. However, GhKNOX1s-silenced plants maintained the wild-type okra leaves. A novel dissected-like leaf in A. thaliana was further generated by crossing plants constitutively expressing GhOKRA with either as1-101 or as2-101 mutant plants. The dissected-like leaves showed two different leaf vein patterns. This report reveals that the LMI1-like and KNOX1 genes coordinately control leaf development, and different combinations of these genes produce diverse leaf shapes including broad leaves, lobed leaves and compound leaves. This is the first report on the artificial generation of compound leaves from simple leaves in cotton.


Assuntos
Genes de Plantas/genética , Proteínas de Homeodomínio/genética , Magnoliopsida/crescimento & desenvolvimento , Magnoliopsida/genética , Desenvolvimento Vegetal/genética , Folhas de Planta/crescimento & desenvolvimento , Proteínas de Plantas/genética , Abelmoschus , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Clonagem Molecular , Regulação da Expressão Gênica no Desenvolvimento , Inativação Gênica , Genes Homeobox/genética , Gossypium , Proteínas de Homeodomínio/classificação , Meristema , Filogenia , Folhas de Planta/anatomia & histologia , Proteínas de Plantas/classificação , Fatores de Transcrição/genética
19.
Mol Biotechnol ; 61(2): 153-172, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30600447

RESUMO

Abiotic stresses such as extreme heat, cold, drought, and salt have brought alteration in plant growth and development, threatening crop yield and quality leading to global food insecurity. Many factors plays crucial role in regulating various plant growth and developmental processes during abiotic stresses. Ethylene response factors (ERFs) are AP2/ERF superfamily proteins belonging to the largest family of transcription factors known to participate during multiple abiotic stress tolerance such as salt, drought, heat, and cold with well-conserved DNA-binding domain. Several extensive studies were conducted on many ERF family proteins in plant species through over-expression and transgenics. However, studies on ERF family proteins with negative regulatory functions are very few. In this review article, we have summarized the mechanism and role of recently studied AP2/ERF-type transcription factors in different abiotic stress responses. We have comprehensively discussed the application of advanced ground-breaking genome engineering tool, CRISPR/Cas9, to edit specific ERFs. We have also highlighted our on-going and published R&D efforts on multiplex CRISPR/Cas9 genome editing of negative regulatory genes for multiple abiotic stress responses in plant and crop models. The overall aim of this review is to highlight the importance of CRISPR/Cas9 and ERFs in developing sustainable multiple abiotic stress tolerance in crop plants.


Assuntos
Produtos Agrícolas/fisiologia , Edição de Genes , Proteínas de Plantas/genética , Estresse Fisiológico , Fatores de Transcrição/genética , Sistemas CRISPR-Cas , Produtos Agrícolas/classificação , Produtos Agrícolas/genética , Regulação da Expressão Gênica de Plantas , Família Multigênica/genética , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas , Transdução de Sinais , Fatores de Transcrição/classificação , Fatores de Transcrição/metabolismo
20.
PLoS One ; 14(1): e0210054, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30699126

RESUMO

Floral bilateral symmetry is one of the most important acquisitions in flower shape evolution in angiosperms. Members of Gesneriaceae possess predominantly zygomorphic flowers yet natural reversal to actinomorphy have independently evolved multiple times. The development of floral bilateral symmetry relies greatly on the gene CYCLOIDEA (CYC). Our reconstructed GCYC phylogeny indicated at least five GCYC duplication events occurred over the evolutionary history of Gesneriaceae. However, the patterns of GCYC expression following the duplications and the role of natural selection on GCYC copies in relation to floral symmetry remained largely unstudied. The Asiatic tribe Trichosporeae contains most reversals to actinomorphy. We thus investigated shifts in GCYC gene expression among selected zygomorphic species (Hemiboea bicornuta and Lysionotus pauciflorus) and species with reversals to actinomorphy (Conandron ramondioides) by RT-PCR. In the actinomorphic C. ramondioides, none of the three copies of GCYC was found expressed in petals implying that the reversal was a loss-of-function event. On the other hand, both zygomorphic species retained one GCYC1 copy that was expressed in the dorsal petals but each species utilized a different copy (GCYC1C for H. bicornuta and GCYC1D for L. pauciflorus). Together with previously published data, it appeared that GCYC1C and GCYC1D copies diversified their expression in a distinct species-specific pattern. To detect whether the selection signal (ω) changed before and after the duplication of GCYC1 in Asiatic Trichosporeae, we reconstructed a GCYC phylogeny using maximum likelihood and Bayesian inference algorithms and examined selection signals using PAML. The PAML analysis detected relaxation from selection right after the GCYC1 duplication (ωpre-duplication = 0.2819, ωpost-duplication = 0.3985) among Asiatic Trichosporeae species. We propose that the selection relaxation after the GCYC1 duplication created an "evolutionary window of flexibility" in which multiple copies were retained with randomly diverged roles for dorsal-specific expressions in association with floral symmetry changes.


Assuntos
Flores/genética , Duplicação Gênica , Genes de Plantas/genética , Magnoliopsida/genética , Seleção Genética , Sequência de Aminoácidos , Evolução Molecular , Flores/anatomia & histologia , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas , Variação Genética , Magnoliopsida/classificação , Filogenia , Proteínas de Plantas/classificação , Proteínas de Plantas/genética , Homologia de Sequência de Aminoácidos , Fatores de Transcrição/genética
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